Starting phenix.real_space_refine on Thu Jul 2 11:51:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k6j_36920/07_2026/8k6j_36920.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k6j_36920/07_2026/8k6j_36920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k6j_36920/07_2026/8k6j_36920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k6j_36920/07_2026/8k6j_36920.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k6j_36920/07_2026/8k6j_36920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k6j_36920/07_2026/8k6j_36920.map" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 6 7.16 5 P 2 5.49 5 S 46 5.16 5 C 5408 2.51 5 N 1482 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8580 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4154 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 502} Chain: "B" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1069 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3130 Classifications: {'peptide': 413} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 388} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 167 Unusual residues: {'HEC': 3, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1} Unresolved non-hydrogen planarities: 25 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1690 SG CYS A 216 51.847 62.208 31.752 1.00139.41 S ATOM 1759 SG CYS A 226 52.396 63.171 35.919 1.00104.53 S ATOM 1730 SG CYS A 222 53.627 67.396 32.557 1.00124.35 S ATOM 1690 SG CYS A 216 51.847 62.208 31.752 1.00139.41 S Time building chain proxies: 1.72, per 1000 atoms: 0.20 Number of scatterers: 8580 At special positions: 0 Unit cell: (103.2, 105.78, 78.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 S 46 16.00 P 2 15.00 O 1636 8.00 N 1482 7.00 C 5408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 241.9 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " Number of angles added : 9 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2008 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 9 sheets defined 42.9% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.756A pdb=" N LYS A 97 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.849A pdb=" N THR A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 138 through 154 removed outlier: 3.563A pdb=" N LEU A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 233 through 244 removed outlier: 4.056A pdb=" N ALA A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 440 through 462 removed outlier: 4.315A pdb=" N VAL A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.724A pdb=" N SER A 492 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.668A pdb=" N THR A 513 " --> pdb=" O THR A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 542 Processing helix chain 'B' and resid 50 through 63 Processing helix chain 'B' and resid 68 through 83 Processing helix chain 'B' and resid 85 through 101 Processing helix chain 'B' and resid 104 through 111 Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'C' and resid 41 through 51 Processing helix chain 'C' and resid 51 through 56 removed outlier: 3.996A pdb=" N CYS C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 105 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 127 through 141 Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.688A pdb=" N TYR C 219 " --> pdb=" O GLN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 256 Processing helix chain 'C' and resid 265 through 274 Processing helix chain 'C' and resid 275 through 278 Processing helix chain 'C' and resid 279 through 292 removed outlier: 3.589A pdb=" N SER C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 324 removed outlier: 3.840A pdb=" N SER C 322 " --> pdb=" O ASN C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 431 through 441 Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.794A pdb=" N LEU C 450 " --> pdb=" O PRO C 446 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.823A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N SER A 7 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA A 282 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA A 282 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N THR A 266 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 267 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL A 254 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.823A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N SER A 7 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA A 282 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 removed outlier: 4.718A pdb=" N HIS A 433 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.308A pdb=" N SER A 347 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR A 368 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 366 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP A 404 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLN A 332 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU A 466 " --> pdb=" O GLN A 332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.199A pdb=" N ASN A 320 " --> pdb=" O GLY A 482 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 482 " --> pdb=" O ASN A 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AA7, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AA8, first strand: chain 'C' and resid 257 through 258 Processing sheet with id=AA9, first strand: chain 'C' and resid 385 through 388 removed outlier: 3.659A pdb=" N ARG C 386 " --> pdb=" O ILE C 393 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 909 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.78: 8724 1.78 - 2.33: 86 2.33 - 2.89: 0 2.89 - 3.44: 0 3.44 - 4.00: 3 Bond restraints: 8813 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.999 -1.699 2.00e-02 2.50e+03 7.22e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.895 -1.637 2.00e-02 2.50e+03 6.70e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.498 -1.265 2.00e-02 2.50e+03 4.00e+03 bond pdb=" C2D HEC C 502 " pdb=" C3D HEC C 502 " ideal model delta sigma weight residual 1.544 1.327 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C2D HEC C 503 " pdb=" C3D HEC C 503 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.14e+02 ... (remaining 8808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.31: 12037 10.31 - 20.63: 2 20.63 - 30.94: 3 30.94 - 41.26: 5 41.26 - 51.57: 2 Bond angle restraints: 12049 Sorted by residual: angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 63.18 51.57 3.00e+00 1.11e-01 2.96e+02 angle pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 103.26 61.43 41.83 3.00e+00 1.11e-01 1.94e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 72.86 39.73 3.00e+00 1.11e-01 1.75e+02 angle pdb="FE1 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 72.09 36.85 35.24 3.00e+00 1.11e-01 1.38e+02 angle pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 71.75 39.57 32.18 3.00e+00 1.11e-01 1.15e+02 ... (remaining 12044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4479 17.89 - 35.78: 519 35.78 - 53.68: 152 53.68 - 71.57: 51 71.57 - 89.46: 12 Dihedral angle restraints: 5213 sinusoidal: 2067 harmonic: 3146 Sorted by residual: dihedral pdb=" CA THR A 164 " pdb=" C THR A 164 " pdb=" N PRO A 165 " pdb=" CA PRO A 165 " ideal model delta harmonic sigma weight residual -180.00 -141.86 -38.14 0 5.00e+00 4.00e-02 5.82e+01 dihedral pdb=" CA LEU C 394 " pdb=" C LEU C 394 " pdb=" N MET C 395 " pdb=" CA MET C 395 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ILE B 159 " pdb=" C ILE B 159 " pdb=" N PRO B 160 " pdb=" CA PRO B 160 " ideal model delta harmonic sigma weight residual -180.00 -155.38 -24.62 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 5210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.482: 1274 3.482 - 6.965: 0 6.965 - 10.447: 0 10.447 - 13.929: 0 13.929 - 17.412: 1 Chirality restraints: 1275 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -6.64 17.41 2.00e-01 2.50e+01 7.58e+03 chirality pdb=" CA PRO A 165 " pdb=" N PRO A 165 " pdb=" C PRO A 165 " pdb=" CB PRO A 165 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CA PRO B 160 " pdb=" N PRO B 160 " pdb=" C PRO B 160 " pdb=" CB PRO B 160 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 1272 not shown) Planarity restraints: 1564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 C 504 " 0.109 2.00e-02 2.50e+03 1.91e-01 1.09e+03 pdb=" C1M U10 C 504 " 0.147 2.00e-02 2.50e+03 pdb=" C2 U10 C 504 " 0.001 2.00e-02 2.50e+03 pdb=" C3 U10 C 504 " -0.026 2.00e-02 2.50e+03 pdb=" C4 U10 C 504 " 0.025 2.00e-02 2.50e+03 pdb=" C5 U10 C 504 " 0.135 2.00e-02 2.50e+03 pdb=" C6 U10 C 504 " 0.175 2.00e-02 2.50e+03 pdb=" C7 U10 C 504 " -0.089 2.00e-02 2.50e+03 pdb=" O2 U10 C 504 " -0.452 2.00e-02 2.50e+03 pdb=" O3 U10 C 504 " 0.284 2.00e-02 2.50e+03 pdb=" O4 U10 C 504 " -0.076 2.00e-02 2.50e+03 pdb=" O5 U10 C 504 " -0.231 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 U10 C 504 " 0.014 2.00e-02 2.50e+03 2.40e-01 7.17e+02 pdb=" C11 U10 C 504 " -0.193 2.00e-02 2.50e+03 pdb=" C7 U10 C 504 " -0.291 2.00e-02 2.50e+03 pdb=" C8 U10 C 504 " 0.400 2.00e-02 2.50e+03 pdb=" C9 U10 C 504 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 U10 C 504 " 0.103 2.00e-02 2.50e+03 8.31e-02 8.62e+01 pdb=" C23 U10 C 504 " -0.130 2.00e-02 2.50e+03 pdb=" C24 U10 C 504 " -0.026 2.00e-02 2.50e+03 pdb=" C25 U10 C 504 " -0.023 2.00e-02 2.50e+03 pdb=" C26 U10 C 504 " 0.077 2.00e-02 2.50e+03 ... (remaining 1561 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 241 2.68 - 3.24: 8423 3.24 - 3.79: 14759 3.79 - 4.35: 19691 4.35 - 4.90: 32317 Nonbonded interactions: 75431 Sorted by model distance: nonbonded pdb=" OG1 THR A 107 " pdb=" O2A FAD A 601 " model vdw 2.130 3.040 nonbonded pdb=" O ARG A 358 " pdb=" OH TYR A 443 " model vdw 2.199 3.040 nonbonded pdb=" N GLU B 136 " pdb=" OE1 GLU B 136 " model vdw 2.204 3.120 nonbonded pdb=" N GLU C 129 " pdb=" OE1 GLU C 129 " model vdw 2.205 3.120 nonbonded pdb=" OD2 ASP A 63 " pdb=" OG1 THR A 66 " model vdw 2.222 3.040 ... (remaining 75426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.980 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.030 1.699 8828 Z= 1.484 Angle : 1.663 75.920 12058 Z= 0.486 Chirality : 0.490 17.412 1275 Planarity : 0.010 0.240 1564 Dihedral : 17.831 89.459 3205 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.49 % Allowed : 23.22 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.26), residues: 1081 helix: 1.88 (0.28), residues: 368 sheet: 0.10 (0.61), residues: 81 loop : -0.09 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 264 TYR 0.014 0.001 TYR A 210 PHE 0.029 0.001 PHE C 156 TRP 0.007 0.001 TRP B 128 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.02989 / 1.48 ( 8813) covalent geometry : angle 1.28417 / 0.48 (12049) hydrogen bonds : bond 0.16717 / 11.95 ( 327) hydrogen bonds : angle 7.00869 / 5.09 ( 909) metal coordination : bond 0.03281 / 1.73 ( 3) metal coordination : angle 38.68817 / 18.04 ( 9) Misc. bond : bond 0.08604 / 4.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7754 (m-40) outliers start: 22 outliers final: 18 residues processed: 108 average time/residue: 0.4406 time to fit residues: 50.9447 Evaluate side-chains 107 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 414 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0030 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.079083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.062568 restraints weight = 16782.854| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.69 r_work: 0.2657 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.234 8828 Z= 0.170 Angle : 1.569 92.611 12058 Z= 0.409 Chirality : 0.063 1.628 1275 Planarity : 0.005 0.058 1564 Dihedral : 10.291 89.319 1312 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.40 % Allowed : 20.16 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.26), residues: 1081 helix: 1.91 (0.28), residues: 381 sheet: -0.19 (0.60), residues: 83 loop : -0.19 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 264 TYR 0.008 0.001 TYR A 232 PHE 0.013 0.001 PHE C 156 TRP 0.006 0.001 TRP A 51 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 8813) covalent geometry : angle 1.03808 / 0.40 (12049) hydrogen bonds : bond 0.03510 / 2.42 ( 327) hydrogen bonds : angle 5.38295 / 4.00 ( 909) metal coordination : bond 0.03724 / 1.78 ( 3) metal coordination : angle 43.08944 / 23.46 ( 9) Misc. bond : bond 0.10127 / 5.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8875 (p) REVERT: B 136 GLU cc_start: 0.8183 (mp0) cc_final: 0.7907 (mp0) REVERT: B 145 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8303 (tm-30) REVERT: C 267 MET cc_start: 0.9052 (tpt) cc_final: 0.8068 (tpt) outliers start: 30 outliers final: 15 residues processed: 117 average time/residue: 0.4718 time to fit residues: 58.9562 Evaluate side-chains 105 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 414 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 75 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 67 optimal weight: 0.0770 chunk 22 optimal weight: 2.9990 chunk 97 optimal weight: 0.0470 chunk 0 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 326 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.076351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.059793 restraints weight = 16630.384| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.66 r_work: 0.2612 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.302 8828 Z= 0.216 Angle : 1.480 80.973 12058 Z= 0.411 Chirality : 0.066 1.728 1275 Planarity : 0.005 0.052 1564 Dihedral : 9.951 89.513 1297 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.62 % Allowed : 20.39 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.26), residues: 1081 helix: 1.84 (0.28), residues: 386 sheet: -0.52 (0.59), residues: 83 loop : -0.24 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 264 TYR 0.013 0.001 TYR A 210 PHE 0.017 0.001 PHE A 80 TRP 0.009 0.001 TRP B 128 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 ( 8813) covalent geometry : angle 1.05305 / 0.40 (12049) hydrogen bonds : bond 0.03469 / 2.39 ( 327) hydrogen bonds : angle 5.11313 / 3.79 ( 909) metal coordination : bond 0.00824 / 0.40 ( 3) metal coordination : angle 38.10558 / 21.66 ( 9) Misc. bond : bond 0.12424 / 7.57 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8969 (p) REVERT: A 175 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8230 (mtt) REVERT: B 113 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8382 (ttmm) REVERT: B 136 GLU cc_start: 0.8195 (mp0) cc_final: 0.7943 (mp0) REVERT: B 145 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8552 (tm-30) REVERT: C 267 MET cc_start: 0.9235 (tpt) cc_final: 0.7693 (tpt) REVERT: C 437 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7796 (tp-100) REVERT: C 443 LYS cc_start: 0.8553 (mmpt) cc_final: 0.7720 (mttp) outliers start: 32 outliers final: 17 residues processed: 109 average time/residue: 0.4499 time to fit residues: 52.4323 Evaluate side-chains 107 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 437 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 89 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.077906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.061419 restraints weight = 16859.968| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.71 r_work: 0.2635 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.248 8828 Z= 0.162 Angle : 1.467 81.671 12058 Z= 0.398 Chirality : 0.062 1.606 1275 Planarity : 0.004 0.051 1564 Dihedral : 9.647 89.029 1296 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.62 % Allowed : 20.72 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.26), residues: 1081 helix: 1.99 (0.28), residues: 382 sheet: -0.59 (0.59), residues: 83 loop : -0.21 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 264 TYR 0.009 0.001 TYR A 210 PHE 0.012 0.001 PHE A 270 TRP 0.007 0.001 TRP B 128 HIS 0.002 0.000 HIS C 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 8813) covalent geometry : angle 1.02515 / 0.39 (12049) hydrogen bonds : bond 0.03015 / 2.07 ( 327) hydrogen bonds : angle 4.90031 / 3.63 ( 909) metal coordination : bond 0.00453 / 0.22 ( 3) metal coordination : angle 38.43680 / 21.99 ( 9) Misc. bond : bond 0.10869 / 6.38 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8982 (p) REVERT: A 175 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8063 (mtt) REVERT: A 192 SER cc_start: 0.8774 (p) cc_final: 0.8568 (p) REVERT: A 211 ASP cc_start: 0.8768 (t0) cc_final: 0.8123 (t0) REVERT: B 91 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8716 (mppt) REVERT: B 136 GLU cc_start: 0.8231 (mp0) cc_final: 0.7941 (mp0) REVERT: C 395 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8173 (tpt) outliers start: 32 outliers final: 14 residues processed: 112 average time/residue: 0.4725 time to fit residues: 56.6047 Evaluate side-chains 108 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 92 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 53 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.076899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.060344 restraints weight = 16863.725| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.71 r_work: 0.2627 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.283 8828 Z= 0.186 Angle : 1.504 82.088 12058 Z= 0.404 Chirality : 0.062 1.575 1275 Planarity : 0.005 0.054 1564 Dihedral : 9.556 89.560 1296 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.28 % Allowed : 21.63 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.26), residues: 1081 helix: 1.89 (0.28), residues: 389 sheet: -0.61 (0.59), residues: 83 loop : -0.25 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 264 TYR 0.010 0.001 TYR A 210 PHE 0.016 0.001 PHE A 80 TRP 0.008 0.001 TRP B 128 HIS 0.002 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 ( 8813) covalent geometry : angle 1.03794 / 0.39 (12049) hydrogen bonds : bond 0.03079 / 2.12 ( 327) hydrogen bonds : angle 4.86186 / 3.61 ( 909) metal coordination : bond 0.00358 / 0.18 ( 3) metal coordination : angle 39.85591 / 22.83 ( 9) Misc. bond : bond 0.11387 / 6.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8970 (p) REVERT: A 175 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8183 (mtt) REVERT: A 211 ASP cc_start: 0.8808 (t0) cc_final: 0.8168 (t0) REVERT: A 462 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8175 (mtt) REVERT: B 94 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8386 (mtm180) REVERT: B 136 GLU cc_start: 0.8227 (mp0) cc_final: 0.7893 (mp0) REVERT: B 145 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8479 (tm-30) REVERT: C 139 MET cc_start: 0.9005 (mmp) cc_final: 0.8672 (mmp) REVERT: C 267 MET cc_start: 0.9206 (tpt) cc_final: 0.7609 (tpt) REVERT: C 395 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8154 (tpt) outliers start: 29 outliers final: 15 residues processed: 109 average time/residue: 0.4737 time to fit residues: 55.1895 Evaluate side-chains 111 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 103 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 106 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.079369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.063004 restraints weight = 16579.828| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.67 r_work: 0.2678 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.204 8828 Z= 0.140 Angle : 1.425 82.319 12058 Z= 0.393 Chirality : 0.060 1.545 1275 Planarity : 0.004 0.050 1564 Dihedral : 9.332 89.636 1295 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.17 % Allowed : 21.86 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.26), residues: 1081 helix: 2.11 (0.28), residues: 381 sheet: -0.48 (0.60), residues: 83 loop : -0.23 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 264 TYR 0.010 0.001 TYR A 79 PHE 0.012 0.001 PHE A 270 TRP 0.005 0.001 TRP A 51 HIS 0.002 0.000 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 8813) covalent geometry : angle 1.01656 / 0.38 (12049) hydrogen bonds : bond 0.02721 / 1.87 ( 327) hydrogen bonds : angle 4.71265 / 3.50 ( 909) metal coordination : bond 0.00283 / 0.14 ( 3) metal coordination : angle 36.58172 / 20.94 ( 9) Misc. bond : bond 0.09110 / 5.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8927 (p) REVERT: A 175 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7910 (mtt) REVERT: A 192 SER cc_start: 0.8731 (p) cc_final: 0.8519 (p) REVERT: A 211 ASP cc_start: 0.8675 (t0) cc_final: 0.7728 (t0) REVERT: A 419 LEU cc_start: 0.9058 (tp) cc_final: 0.8808 (tm) REVERT: A 469 MET cc_start: 0.8964 (ttt) cc_final: 0.8647 (tpp) REVERT: A 505 ASN cc_start: 0.8876 (t0) cc_final: 0.8588 (t160) REVERT: B 94 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8318 (mtm180) REVERT: B 136 GLU cc_start: 0.8271 (mp0) cc_final: 0.7916 (mp0) REVERT: C 139 MET cc_start: 0.9037 (mmp) cc_final: 0.8668 (mmp) REVERT: C 267 MET cc_start: 0.9155 (tpt) cc_final: 0.7601 (tpt) REVERT: C 395 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8056 (ttt) REVERT: C 443 LYS cc_start: 0.8432 (mmpt) cc_final: 0.7644 (mttp) outliers start: 28 outliers final: 13 residues processed: 115 average time/residue: 0.4343 time to fit residues: 53.6944 Evaluate side-chains 110 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.078681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.062791 restraints weight = 16791.336| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.61 r_work: 0.2673 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.218 8828 Z= 0.154 Angle : 1.454 82.156 12058 Z= 0.399 Chirality : 0.061 1.559 1275 Planarity : 0.004 0.052 1564 Dihedral : 9.249 89.220 1293 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.94 % Allowed : 22.31 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.26), residues: 1081 helix: 2.11 (0.28), residues: 382 sheet: -0.51 (0.60), residues: 83 loop : -0.21 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 264 TYR 0.015 0.001 TYR A 79 PHE 0.017 0.001 PHE C 210 TRP 0.006 0.001 TRP B 128 HIS 0.002 0.000 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 8813) covalent geometry : angle 1.02770 / 0.39 (12049) hydrogen bonds : bond 0.02784 / 1.92 ( 327) hydrogen bonds : angle 4.70650 / 3.50 ( 909) metal coordination : bond 0.00294 / 0.14 ( 3) metal coordination : angle 37.65201 / 21.57 ( 9) Misc. bond : bond 0.09497 / 5.67 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8995 (p) REVERT: A 175 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8188 (mtt) REVERT: A 192 SER cc_start: 0.8735 (p) cc_final: 0.8527 (p) REVERT: A 211 ASP cc_start: 0.8816 (t0) cc_final: 0.7878 (t0) REVERT: A 419 LEU cc_start: 0.9133 (tp) cc_final: 0.8885 (tm) REVERT: A 469 MET cc_start: 0.8968 (ttt) cc_final: 0.8615 (tpp) REVERT: A 505 ASN cc_start: 0.8953 (t0) cc_final: 0.8653 (t160) REVERT: B 55 MET cc_start: 0.8507 (tpp) cc_final: 0.8292 (mmp) REVERT: B 86 PHE cc_start: 0.8935 (t80) cc_final: 0.8439 (t80) REVERT: B 91 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8694 (mppt) REVERT: B 136 GLU cc_start: 0.8300 (mp0) cc_final: 0.7943 (mp0) REVERT: C 139 MET cc_start: 0.9043 (mmp) cc_final: 0.8676 (mmp) REVERT: C 395 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8046 (tpt) REVERT: C 443 LYS cc_start: 0.8466 (mmpt) cc_final: 0.7658 (mttp) outliers start: 26 outliers final: 13 residues processed: 109 average time/residue: 0.4511 time to fit residues: 52.9169 Evaluate side-chains 110 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 447 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 100 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.077868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.061366 restraints weight = 16698.534| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 2.67 r_work: 0.2645 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.244 8828 Z= 0.172 Angle : 1.486 82.145 12058 Z= 0.404 Chirality : 0.062 1.566 1275 Planarity : 0.005 0.056 1564 Dihedral : 9.233 88.198 1293 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.72 % Allowed : 22.88 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.26), residues: 1081 helix: 2.02 (0.28), residues: 387 sheet: -0.48 (0.60), residues: 83 loop : -0.26 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 264 TYR 0.022 0.001 TYR A 79 PHE 0.022 0.001 PHE C 210 TRP 0.008 0.001 TRP B 128 HIS 0.003 0.000 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 8813) covalent geometry : angle 1.03765 / 0.39 (12049) hydrogen bonds : bond 0.02890 / 1.99 ( 327) hydrogen bonds : angle 4.73719 / 3.53 ( 909) metal coordination : bond 0.00292 / 0.14 ( 3) metal coordination : angle 38.92792 / 22.31 ( 9) Misc. bond : bond 0.10277 / 6.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.7379 (OUTLIER) cc_final: 0.6832 (t) REVERT: A 108 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8993 (p) REVERT: A 175 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8208 (mtt) REVERT: A 192 SER cc_start: 0.8750 (p) cc_final: 0.8543 (p) REVERT: A 211 ASP cc_start: 0.8855 (t0) cc_final: 0.8216 (t0) REVERT: A 419 LEU cc_start: 0.9154 (tp) cc_final: 0.8893 (tm) REVERT: A 469 MET cc_start: 0.9016 (ttt) cc_final: 0.8636 (tpp) REVERT: A 505 ASN cc_start: 0.8996 (t0) cc_final: 0.8713 (t160) REVERT: B 55 MET cc_start: 0.8521 (tpp) cc_final: 0.8297 (mmp) REVERT: B 86 PHE cc_start: 0.8912 (t80) cc_final: 0.8454 (t80) REVERT: B 91 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8692 (mppt) REVERT: B 94 ARG cc_start: 0.8702 (mtm180) cc_final: 0.8349 (mtm180) REVERT: B 136 GLU cc_start: 0.8299 (mp0) cc_final: 0.7939 (mp0) REVERT: C 139 MET cc_start: 0.9035 (mmp) cc_final: 0.8658 (mmp) REVERT: C 267 MET cc_start: 0.9203 (tpt) cc_final: 0.7564 (tpt) REVERT: C 395 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.7955 (tpt) REVERT: C 443 LYS cc_start: 0.8483 (mmpt) cc_final: 0.7697 (mttp) outliers start: 24 outliers final: 12 residues processed: 109 average time/residue: 0.4628 time to fit residues: 53.9769 Evaluate side-chains 108 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 22 optimal weight: 0.0770 chunk 3 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 16 optimal weight: 0.0570 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.078145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.062072 restraints weight = 16924.008| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.62 r_work: 0.2655 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.219 8828 Z= 0.151 Angle : 1.449 82.293 12058 Z= 0.399 Chirality : 0.061 1.548 1275 Planarity : 0.005 0.058 1564 Dihedral : 9.155 88.190 1293 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.15 % Allowed : 23.67 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.26), residues: 1081 helix: 2.03 (0.28), residues: 387 sheet: -0.46 (0.60), residues: 83 loop : -0.27 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 264 TYR 0.020 0.001 TYR A 79 PHE 0.023 0.001 PHE C 210 TRP 0.005 0.001 TRP A 51 HIS 0.002 0.000 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 8813) covalent geometry : angle 1.02704 / 0.39 (12049) hydrogen bonds : bond 0.02733 / 1.88 ( 327) hydrogen bonds : angle 4.68178 / 3.49 ( 909) metal coordination : bond 0.00240 / 0.12 ( 3) metal coordination : angle 37.40966 / 21.41 ( 9) Misc. bond : bond 0.09859 / 5.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8905 (p) REVERT: A 175 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8026 (mtt) REVERT: A 192 SER cc_start: 0.8659 (p) cc_final: 0.8450 (p) REVERT: A 211 ASP cc_start: 0.8805 (t0) cc_final: 0.8147 (t0) REVERT: A 419 LEU cc_start: 0.9075 (tp) cc_final: 0.8816 (tm) REVERT: A 469 MET cc_start: 0.8959 (ttt) cc_final: 0.8574 (tpp) REVERT: A 505 ASN cc_start: 0.8958 (t0) cc_final: 0.8656 (t160) REVERT: B 86 PHE cc_start: 0.8794 (t80) cc_final: 0.8378 (t80) REVERT: B 91 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8677 (mppt) REVERT: B 94 ARG cc_start: 0.8619 (mtm180) cc_final: 0.8250 (mtm180) REVERT: B 136 GLU cc_start: 0.8277 (mp0) cc_final: 0.7926 (mp0) REVERT: C 139 MET cc_start: 0.8975 (mmp) cc_final: 0.8604 (mmp) REVERT: C 267 MET cc_start: 0.9125 (tpt) cc_final: 0.7468 (tpt) REVERT: C 395 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.7912 (tpt) outliers start: 19 outliers final: 12 residues processed: 106 average time/residue: 0.5720 time to fit residues: 64.8313 Evaluate side-chains 108 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 5 optimal weight: 0.0170 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.078379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.062395 restraints weight = 16895.961| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.63 r_work: 0.2667 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.212 8828 Z= 0.150 Angle : 1.448 82.281 12058 Z= 0.401 Chirality : 0.061 1.547 1275 Planarity : 0.005 0.064 1564 Dihedral : 9.123 87.059 1292 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.15 % Allowed : 23.67 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.26), residues: 1081 helix: 2.16 (0.28), residues: 382 sheet: -0.41 (0.60), residues: 83 loop : -0.22 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 264 TYR 0.009 0.001 TYR A 443 PHE 0.027 0.001 PHE C 210 TRP 0.006 0.001 TRP A 51 HIS 0.002 0.000 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 8813) covalent geometry : angle 1.03326 / 0.39 (12049) hydrogen bonds : bond 0.02690 / 1.85 ( 327) hydrogen bonds : angle 4.64747 / 3.47 ( 909) metal coordination : bond 0.00252 / 0.12 ( 3) metal coordination : angle 37.14762 / 21.26 ( 9) Misc. bond : bond 0.10132 / 5.90 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8901 (p) REVERT: A 175 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8066 (mtt) REVERT: A 192 SER cc_start: 0.8649 (p) cc_final: 0.8446 (p) REVERT: A 211 ASP cc_start: 0.8819 (t0) cc_final: 0.8165 (t0) REVERT: A 419 LEU cc_start: 0.9075 (tp) cc_final: 0.8835 (tm) REVERT: A 468 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7871 (mt-10) REVERT: A 469 MET cc_start: 0.8958 (ttt) cc_final: 0.8591 (tpp) REVERT: A 505 ASN cc_start: 0.8959 (t0) cc_final: 0.8656 (t160) REVERT: B 86 PHE cc_start: 0.8783 (t80) cc_final: 0.8482 (t80) REVERT: B 94 ARG cc_start: 0.8630 (mtm180) cc_final: 0.8269 (mtm180) REVERT: B 136 GLU cc_start: 0.8281 (mp0) cc_final: 0.7932 (mp0) REVERT: C 139 MET cc_start: 0.8979 (mmp) cc_final: 0.8611 (mmp) REVERT: C 267 MET cc_start: 0.9130 (tpt) cc_final: 0.7449 (tpt) REVERT: C 395 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.7864 (tpt) REVERT: C 443 LYS cc_start: 0.8511 (mmpt) cc_final: 0.7599 (mttp) outliers start: 19 outliers final: 12 residues processed: 106 average time/residue: 0.5024 time to fit residues: 57.3536 Evaluate side-chains 107 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 395 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.077785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.061649 restraints weight = 16964.188| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.63 r_work: 0.2651 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.233 8828 Z= 0.167 Angle : 1.477 82.230 12058 Z= 0.404 Chirality : 0.061 1.556 1275 Planarity : 0.004 0.053 1564 Dihedral : 8.984 86.763 1291 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.27 % Allowed : 23.33 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.26), residues: 1081 helix: 2.02 (0.28), residues: 388 sheet: -0.43 (0.60), residues: 83 loop : -0.26 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 264 TYR 0.009 0.001 TYR A 210 PHE 0.026 0.001 PHE C 210 TRP 0.008 0.001 TRP B 128 HIS 0.003 0.000 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 ( 8813) covalent geometry : angle 1.04098 / 0.39 (12049) hydrogen bonds : bond 0.02800 / 1.93 ( 327) hydrogen bonds : angle 4.67879 / 3.49 ( 909) metal coordination : bond 0.00251 / 0.12 ( 3) metal coordination : angle 38.34550 / 21.97 ( 9) Misc. bond : bond 0.11006 / 6.46 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2319.90 seconds wall clock time: 40 minutes 17.71 seconds (2417.71 seconds total)